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xdeupi's modeling [47 articles]

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  • Activation of the mu opioid receptor involves conformational rearrangements of multiple transmembrane domains.
    Biochemistry, Vol. 47, No. 40. (7 October 2008), pp. 10576-10586.
    by W Xu, A Sanz, L Pardo, LY Liu-Chen
    posted to switch opioid modeling cys_scanning activation by xdeupi on 2008-10-15 10:57:26 as **
  • The specificity of binding of glycoprotein hormones to their receptors.
    Cellular and molecular life sciences : CMLS (26 April 2008)
    by G Caltabiano, M Campillo, A De Leener, G Smits, G Vassart, S Costagliola, L Pardo
    posted to activation hormone modeling thyrotropin by xdeupi on 2008-05-03 17:06:33 as ** along with 1 group LabCompMed
  • notes Protein-Protein Docking with Backbone Flexibility
    Journal of Molecular Biology, Vol. 373, No. 2. (19 October 2007), pp. 503-519.
    by Chu Wang, Philip Bradley, David Baker
    posted to docking flexibility modeling theory by xdeupi on 2008-04-07 14:23:45 as ** along with 4 people and 2 groups csrocha barry jwm Ema structural_bioinformatics Bioinformatics
  • notes Protein-Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations
    Journal of Molecular Biology, Vol. 331, No. 1. (1 August 2003), pp. 281-299.
    by Jeffrey J Gray, Stewart Moughon, Chu Wang, Ora Schueler-Furman, Brian Kuhlman, Carol A Rohl, David Baker
    posted to dimer docking modeling theory by xdeupi on 2008-04-07 14:18:56 as ** along with 4 people ima bluvsh1 selrac timg
  • A concept for G protein activation by G protein-coupled receptor dimers: the transducin/rhodopsin interface.
    Photochem Photobiol Sci, Vol. 3, No. 6. (June 2004), pp. 628-638.
    by S Filipek, KA Krzysko, D Fotiadis, Y Liang, DA Saperstein, A Engel, K Palczewski
    posted to active-state gproteins modeling rhodopsin structure by xdeupi on 2007-07-11 16:54:09 as ** along with 1 person and 1 group cen4ik LabCompMed
  • Refinement of a homology model of the mu-opioid receptor using distance constraints from intrinsic and engineered zinc-binding sites.
    Biochemistry, Vol. 43, No. 27. (13 July 2004), pp. 8700-8710.
    by CB Fowler, ID Pogozheva, H LeVine, HI Mosberg
    posted to active-state modeling opioid structure theory by xdeupi on 2007-07-11 16:51:53 as ** along with 1 person and 1 group merj LabCompMed
  • Complex of an active mu-opioid receptor with a cyclic peptide agonist modeled from experimental constraints.
    Biochemistry, Vol. 43, No. 50. (21 December 2004), pp. 15796-15810.
    by CB Fowler, ID Pogozheva, AL Lomize, H LeVine, HI Mosberg
    posted to active-state gproteins modeling opioid structure by xdeupi on 2007-07-11 16:50:15 as ** along with 1 group LabCompMed
  • Modeling of the complex between transducin and photoactivated rhodopsin, a prototypical G-protein-coupled receptor.
    Biochemistry, Vol. 46, No. 16. (24 April 2007), pp. 4734-4744.
    by GV Nikiforovich, CM Taylor, GR Marshall
    posted to gproteins modeling rhodopsin by xdeupi on 2007-07-11 11:05:58 as ** along with 1 group LabCompMed
  • Performance of the general amber force field in modeling aqueous POPC membrane bilayers.
    J Comput Chem, Vol. 28, No. 12. (12 April 2007), pp. 2051-2058.
    by Balázs Jójárt, Tamás A A Martinek
    posted to amber dynamics md membrane modeling theory by xdeupi on 2007-06-26 13:32:45 as ** along with 3 people and 1 group dimka easybakemuffin viktor21614 LabCompMed
  • Refinement of Protein Structures by Iterative Comparative Modeling and CryoEM Density Fitting
    Journal of Molecular Biology, Vol. 357, No. 5. (14 April 2006), pp. 1655-1668.
    by Maya Topf, Matthew L Baker, Marc A Marti-Renom, Wah Chiu, Andrej Sali
    posted to crystallography em modeling structure theory by xdeupi on 2007-06-12 11:28:16 as ** along with 1 group LabCompMed
  • An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies
    Protein Eng., Vol. 9, No. 11. (1996), pp. 1063-1065.
    by Lawrence A Kelley, Stephen P Gardner, Michael J Sutcliffe
    posted to dynamics helix md modeling structure theory by xdeupi on 2007-05-31 10:31:28 as ** along with 1 group LabCompMed
  • Structural models of class a g protein-coupled receptors as a tool for drug design: insights on transmembrane bundle plasticity.
    Curr Top Med Chem, Vol. 7, No. 10. (2007), pp. 999-1006.
    by X Deupi Nicole Dölker María Luz López-Rodríguez Mercedes Campillo Juan A Ballesteros And Leonardo Pardo, N Dölker, ML López-Rodríguez, M Campillo, JA Ballesteros, L Pardo
    posted to binding gpcr modeling plasticity structure by xdeupi on 2007-05-28 08:51:54 as ** along with 1 group LabCompMed
  • Chromophore Channeling in the G-Protein Coupled Receptor Rhodopsin.
    J Am Chem Soc (15 May 2007)
    by Ting Wang, Yong Duan
    posted to activation agonist amber binding ligands md modeling rhodopsin by xdeupi on 2007-05-21 10:04:04 as ***** along with 1 group LabCompMed
  • Computational prediction of atomic structures of helical membrane proteins aided by EM maps.
    Biophys J (11 May 2007)
    by Julio A A Kovacs, Mark Yeager, Ruben Abagyan
    posted to crystallography em membrane_proteins modeling structure by xdeupi on 2007-05-21 09:41:00 as ** along with 1 person and 1 group thaliana LabCompMed
  • Understanding interactions of gastric inhibitory polypeptide (GIP) with its G-protein coupled receptor through NMR and molecular modeling.
    J Pept Sci, Vol. 13, No. 5. (16 April 2007), pp. 287-300.
    by Alpeshkumar K K Malde, Sudha S S Srivastava, Evans C C Coutinho
    posted to modeling nmr nterm by xdeupi on 2007-04-23 10:26:25 as ** along with 1 group LabCompMed
  • Peptide design and structural characterization of a GPCR loop mimetic.
    Biopolymers (18 April 2007)
    by Truc-Chi T C Pham, Richard W W Kriwacki, Abby L L Parrill
    posted to gpcr loops modeling structure by xdeupi on 2007-04-23 10:24:23 as ** along with 1 group LabCompMed
  • Pharmacogenomic and structural analysis of constitutive g protein-coupled receptor activity.
    Annu Rev Pharmacol Toxicol, Vol. 47 (2007), pp. 53-87.
    by MJ Smit, HF Vischer, RA Bakker, A Jongejan, H Timmerman, L Pardo, R Leurs
    posted to activation disease gpcr modeling review structure switch by xdeupi on 2007-04-17 12:35:15 as ** along with 1 group LabCompMed
  • Atomic-level characterization of disordered protein ensembles
    Current Opinion in Structural Biology, Vol. 17, No. 1. (February 2007), pp. 3-14.
    by Tanja Mittag, Julie D Forman-Kay
    posted to crystallography cterm disorder folding icl3 modeling nmr structure by xdeupi on 2007-03-27 16:17:12 as ** along with 4 people and 1 group apaydin cactus biehl allmensch LabCompMed
  • Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling.
    J Comput Aided Mol Des, Vol. 20, No. 7-8. (g 2006), pp. 449-461.
    by F Fanelli, PG De Benedetti
    posted to gpcr modeling review by xdeupi on 2007-03-26 10:31:45 as ** along with 1 group LabCompMed
  • Setting up and running molecular dynamics simulations of membrane proteins.
    Methods, Vol. 41, No. 4. (April 2007), pp. 475-488.
    by C Kandt, WL Ash, D Peter Tieleman
    posted to dynamics md membrane modeling review transmembrane by xdeupi on 2007-03-26 10:15:17 as ***** along with 1 person and 2 groups sobolevnrm LabCompMed baker-group
  • Method To Assess Packing Quality of Transmembrane alpha-Helices in Proteins. 1. Parametrization Using Structural Data.
    J Chem Inf Model (20 March 2007)
    by Anton O Chugunov, Valery N Novoseletsky, Dmitry E Nolde, Alexander S Arseniev, Roman G Efremov
    posted to gpcr membrane_proteins modeling structure by xdeupi on 2007-03-26 10:07:02 as ** along with 1 person and 1 group superpyrin LabCompMed
  • Predisposition of the dark state of rhodopsin to functional changes in structure
    Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 4. (2006), pp. 970-983.
    by Basak Isin, AJ Rader, Harpreet K Dhiman, Judith Klein-Seetharaman, Ivet Bahar
    posted to activation dynamics modeling rhodopsin by xdeupi on 2007-02-26 09:19:19 as **** along with 1 person and 1 group aqeel LabCompMed
  • How a small change in retinal leads to G-protein activation: initial events suggested by molecular dynamics calculations.
    Proteins, Vol. 66, No. 3. (15 February 2007), pp. 559-574.
    by PS Crozier, MJ Stevens, TB Woolf
    posted to activation dynamics md modeling rhodopsin switch by xdeupi on 2007-02-26 09:15:15 as **** along with 1 group LabCompMed
  • Catalytic mechanism of cyclophilin as observed in molecular dynamics simulations: pathway prediction and reconciliation of X-ray crystallographic and NMR solution data.
    Protein Sci, Vol. 15, No. 11. (November 2006), pp. 2544-2551.
    by D Trzesniak, WF van Gunsteren
    posted to crystallography dynamics modeling by xdeupi on 2007-02-20 09:52:40 as ** along with 1 group LabCompMed
  • notes Solvation parameters for amino acids
    Journal of Computational Chemistry, Vol. 20, No. 4. (1999), pp. 428-442.
    by Brian J Smith
    posted to solvation modeling by xdeupi on 2007-01-12 12:48:19 as ** along with 1 person and 1 group papatonyhill LabCompMed
  • GluVII:06--a highly conserved and selective anchor point for non-peptide ligands in chemokine receptors.
    Curr Top Med Chem, Vol. 6, No. 13. (2006), pp. 1319-1333.
    by MM Rosenkilde, TW Schwartz
    posted to modeling ligands ionic chemokine binding agonist by xdeupi on 2007-01-10 14:45:13 as ** along with 1 group LabCompMed
  • A structure-based simulation approach for electron paramagnetic resonance spectra using molecular and stochastic dynamics simulations.
    Biophys J, Vol. 91, No. 7. (1 October 2006), pp. 2647-2664.
    by C Beier, HJ Steinhoff
    posted to dynamics loops md modeling spin_labeling structure by xdeupi on 2006-10-30 18:37:07 as ** along with 1 group LabCompMed
  • dummy
    by Dummy
    posted to 5ht1a activation agonist amber amine arrestin b2ar bimane binding cam ccr5 channel chemokine chimera crystallography cterm cxcr1 d250 dimer disease drug dry dynamics ecl2 evolution expression fluorescence folding fret genome gly gpcr gproteins hbond helix helix8 histamine hormone icl3 imaging internalization ionic leukotriene lhr ligands lipids lock loops md membrane modeling mutation n745 n749 nmr no-tag npxxy nterm opioid pharmacology polymorphism pro-kink protonation review rhodopsin s542 sequence ser spin_labeling structure switch test thr thyrotropin tm2 tm3 tm5 tm6 tm7 toggle transmembrane trp txp w648 by xdeupi on 2006-10-30 12:30:16 as ** along with 2 people and 1 group jessicaopacic ivanrt LabCompMed
  • Modeling and active site refinement for G protein-coupled receptors: application to the beta-2 adrenergic receptor.
    J Comput Aided Mol Des (13 October 2006)
    by Stanley R Krystek, S R Kimura, Andrew J Tebben
    posted to b2ar binding drug ligands modeling pharmacology by xdeupi on 2006-10-27 09:43:03 as ** along with 1 person and 1 group daevans LabCompMed
  • Helix-packing motifs in membrane proteins.
    Proc Natl Acad Sci U S A (5 September 2006)
    by R F S F Walters, W F F Degrado
    posted to folding helix membrane modeling sequence structure transmembrane by xdeupi on 2006-09-13 10:25:08 as **** along with 5 people and 1 group hc5428 thaliana dgront sebk chgjb LabCompMed
  • Asymmetric stability among the transmembrane helices of lactose permease.
    Biochemistry, Vol. 45, No. 26. (4 July 2006), pp. 8088-8095.
    by M Bennett, R D'Rozario, MS Sansom, PL Yeagle
    posted to activation dynamics helix md modeling structure transmembrane by xdeupi on 2006-09-05 11:09:02 as ** along with 1 group LabCompMed
  • Novel mutants of the human beta1-adrenergic receptor reveal amino acids relevant for receptor activation.
    J Biol Chem, Vol. 281, No. 26. (30 June 2006), pp. 18120-18125.
    by B Behr, C Hoffmann, G Ottolina, KN Klotz
    posted to activation agonist b2ar binding drug ligands modeling mutation pharmacology structure by xdeupi on 2006-09-05 11:05:20 as *** along with 1 group LabCompMed
  • Structure and dynamics of dark-state bovine rhodopsin revealed by chemical cross-linking and high-resolution mass spectrometry.
    Protein Sci, Vol. 15, No. 6. (June 2006), pp. 1303-1317.
    by RB Jacobsen, KL Sale, MJ Ayson, P Novak, J Hong, P Lane, NL Wood, GH Kruppa, MM Young, JS Schoeniger
    posted to dynamics gpcr modeling rhodopsin structure by xdeupi on 2006-09-05 10:52:14 as ** along with 1 group LabCompMed
  • ZPRED: Predicting the distance to the membrane center for residues in alpha-helical membrane proteins.
    Bioinformatics, Vol. 22, No. 14. (15 July 2006)
    by E Granseth, H Viklund, A Elofsson
    posted to helix loops membrane modeling structure transmembrane by xdeupi on 2006-09-05 10:16:39 as ***** along with 2 people and 1 group thaliana chrn LabCompMed
  • TRAJELIX: A Computational Tool for the Geometric Characterization of Protein Helices During Molecular Dynamics Simulations
    Journal of Computer-Aided Molecular Design, Vol. 20, No. 2. (February 2006), pp. 97-107.
    by Mezei, Mihaly, Filizola, Marta
    posted to md modeling structure transmembrane by xdeupi on 2006-07-21 12:20:38 as ** along with 1 group LabCompMed
  • Metal Ion Site Engineering Indicates a Global Toggle Switch Model for Seven-transmembrane Receptor Activation.
    J Biol Chem, Vol. 281, No. 25. (23 June 2006), pp. 17337-17346.
    by CE Elling, TM Frimurer, LO Gerlach, R Jorgensen, B Holst, TW Schwartz
    posted to activation b2ar modeling pro-kink structure switch toggle transmembrane by xdeupi on 2006-07-04 12:17:13 as read along with 1 person and 1 group IrinaMoreira LabCompMed
  • Molecular mechanism of 7TM receptor activation--a global toggle switch model.
    Annu Rev Pharmacol Toxicol, Vol. 46 (2006), pp. 481-519.
    by TW Schwartz, TM Frimurer, B Holst, MM Rosenkilde, CE Elling
    posted to activation gpcr helix modeling switch toggle by xdeupi on 2006-06-01 14:31:34 as read along with 1 person and 1 group superpyrin LabCompMed
  • Toward the active conformations of rhodopsin and the beta2-adrenergic receptor.
    Proteins, Vol. 56, No. 1. (1 July 2004), pp. 67-84.
    by PR Gouldson, NJ Kidley, RP Bywater, G Psaroudakis, HD Brooks, C Diaz, D Shire, CA Reynolds
    posted to activation b2ar modeling rhodopsin structure by xdeupi on 2006-03-08 14:57:08 as ** along with 1 group LabCompMed
  • Molecular evolution of adrenoceptors and dopamine receptors: implications for the binding of catecholamines.
    J Med Chem, Vol. 49, No. 5. (9 March 2006), pp. 1706-1719.
    by H Xhaard, VV Rantanen, T Nyrönen, MS Johnson
    posted to agonist b2ar binding gpcr ligands modeling by xdeupi on 2006-03-06 10:11:30 as **** along with 1 group LabCompMed
  • Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome.
    PLoS Comput Biol, Vol. 2, No. 2. (17 February 2006)
    by Yang Zhang, Mark E E Devries, Jeffrey Skolnick
    posted to genome gpcr modeling structure by xdeupi on 2006-03-01 10:00:31 as ** along with 3 people and 1 group allanlo jfmuggs superpyrin LabCompMed
  • Conformational dynamics of M2 helices in KirBac channels: helix flexibility in relation to gating via molecular dynamics simulations.
    Biochemistry, Vol. 44, No. 44. (8 November 2005), pp. 14586-14594.
    by A Grottesi, C Domene, B Hall, MS Sansom
    posted to activation channel dynamics md membrane modeling transmembrane by xdeupi on 2006-02-20 09:24:41 as read along with 1 person and 1 group dimka LabCompMed
  • Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model.
    J Phys Chem B Condens Matter Mater Surf Interfaces Biophys, Vol. 110, No. 1. (12 January 2006), pp. 548-556.
    by S Tanizaki, M Feig
    posted to dynamics membrane modeling transmembrane by xdeupi on 2006-02-20 09:15:18 as ** along with 2 people and 1 group onufriev dimka LabCompMed
  • Automatic atom type and bond type perception in molecular mechanical calculations.
    J Mol Graph Model (1 February 2006)
    by Junmei Wang, Wei Wang, Peter A A Kollman, David A A Case
    posted to amber dynamics md modeling by xdeupi on 2006-02-13 15:46:26 as ***** along with 5 people and 1 group A_Coletta_Thesis dgruiz nigham marcvanhouteghem AndreaColetta LabCompMed
  • Evaluating Tilt Angles of Membrane-Associated Helices: Comparison of Computational and NMR Techniques
    Biophys. J., Vol. 90, No. 5. (1 March 2006), pp. 1650-1660.
    by Martin B Ulmschneider, Mark S Sansom, Alfredo Di Nola
    posted to helix membrane modeling structure transmembrane by xdeupi on 2006-02-10 09:49:58 as ***** along with 2 people and 1 group thaliana loison LabCompMed
  • Can Conformational Change Be Described by Only a Few Normal Modes?
    Biophys. J., Vol. 90, No. 5. (1 March 2006), pp. 1583-1593.
    by Paula Petrone, Vijay S Pande
    posted to activation dynamics folding modeling by xdeupi on 2006-02-10 09:48:29 as ***** along with 11 people and 7 groups csrocha BragilMassoud barry dimka aqeel shuns yongzhao choonpeng joergkurtwegner daevans LamBras structural_bioinformatics Bioinformatics TSRI_MGL Molecular-Modelling Drug-Design Cheminformatics LabCompMed
  • A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.
    J Comput Chem, Vol. 24, No. 16. (December 2003), pp. 1999-2012.
    by Y Duan, C Wu, S Chowdhury, MC Lee, G Xiong, W Zhang, R Yang, P Cieplak, R Luo, T Lee, J Caldwell, J Wang, P Kollman
    posted to amber dynamics md modeling by xdeupi on 2006-01-24 11:35:18 as **** along with 2 people and 1 group A_Coletta_Thesis schlauchi LabCompMed
  • Homology modeling and molecular dynamics simulations of the mu opioid receptor in a membrane-aqueous system.
    Chembiochem, Vol. 6, No. 5. (May 2005), pp. 853-859.
    by Y Zhang, YY Sham, R Rajamani, J Gao, PS Portoghese
    posted to dynamics modeling opioid by xdeupi on 2006-01-11 11:21:06 as ** along with 2 people and 1 group BragilMassoud apostola LabCompMed
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